genotype.h

#ifndef __gamgee__genotype__
#define __gamgee__genotype__

#include "utils/hts_memory.h"
#include "genotype_encoding_value.h"
#include "genotype_encoding.h"

#include "utils/utils.h"
#include "utils/format_field_type.h"

#include "htslib/vcf.h"

#include <memory>

namespace gamgee {

/**
 * @brief Encodes a genotype.
 */
class Genotype {
  public:
  /**
   * @brief Creates a genotype.
   * @param body The shared memory variant "line" from a vcf, or bcf.
   * @param format_ptr The GT field from the line.
   * @param data_ptr The GT for this sample.
   */
  Genotype(const std::shared_ptr<bcf1_t>& body, const bcf_fmt_t* const format_ptr, const uint8_t* data_ptr);

  /**
   * @brief Moves a genotype.
   * @param other The other genotype object to move.
   */
  Genotype(Genotype&& other) noexcept;

  // only for diploids
  /**
   * @brief Checks if this genotype is any type of heterozygous call.
   * @return True if this GT is a het.
   * @note only for diploids.
   */
  bool is_het() const;
  /**
   * @brief Checks if this genotype is a homozygous call that is non-reference.
   * @return True if this GT is a hom var.
   * @note only for diploids.
   */
  bool is_hom_var() const;
  /**
   * @brief Checks if this genotype is a homozygous call that is reference.
   * @return True if this GT is a hom ref.
   * @note only for diploids.
   */
  bool is_hom_ref() const;

  /**
   * @brief Returns a bit encoding of the first two alleles.
   * @return A bit encoding of the first two alleles.
   * @note only for diploids.
   */
  GenotypeEncoding value() const; // returns the number of the genotype. => 0/1 = 1 | 0/0 = 0 | 1/1 = 2 ... | 0/2

  /**
   * @brief Returns a string decoding of each allele.
   * @param index From [0,size())
   * @return A string decoding of the allele at index.
   */
  GenotypeEncodingValue operator[](const uint32_t index) const;  // getter

  /**
   * @brief Number of alleles in this genotype.
   * @return Number of alleles in this genotype.
   */
  uint32_t size() const;

  /**
   * @brief The alleles in this genotype.
   * @return  The alleles in this genotype as strings.
   */
  vector<string> alleles() const; // returns the actual alleles (e.g. A/T or TG/C or T/T/C or T/T/T/T/T ... )

private:
  const std::shared_ptr<bcf1_t> m_body;
  const bcf_fmt_t* const m_format_ptr;
  const uint8_t* m_data_ptr;

  int32_t allele(const uint32_t allele_index) const;

  template<class TYPE>
  int32_t allele(const uint32_t allele_index) const;

  template<class TYPE>
  vector<string> alleles(TYPE missing, TYPE vector_end) const;

  string allele_string(int32_t allele_int) const;
};

}

#endif